Below is a series of tables and plots detailing the structural variants identified by NAIBR (publication). The variants are given by:
| Name | Description |
|---|---|
| Inversion | a segment that broke off and reattached within the same chromosome, but in reverse orientation |
| Duplication | a type of mutation involving the production of one or more copies of a gene or region of a chromosome |
| Deletion | a type of mutation involving the loss of one or more nucleotides from a segment of DNA |
This report shows overview information.
In the colorful summary boxes are the per-population average number of variants detected by type.
The table below details counts each type of structural variant for every contig for every population.
The table below details the lengths (in bp) of structural variants for every contig for every population.
NAIBR outputs a tab-delimited file with named columns (along with a VCF and a reformatted bedpe file with extra information). The columns of the bedpe file are deciphered as such:
| Column Name | Description |
|---|---|
| Population | Name of the population |
| Chr1 | Name of the contig where the variant starts |
| Break1 | Base-pair position in Chr1 of the start of
the variant |
| Chr2 | Name of the contig where the variant ends |
| Break2 | Base-pair position in Chr2 of the end of
the variant |
| SplitMolecules | Number of split molecules supporting variant |
| DiscordantReads | Number of discordant reads supporting variant |
| Orientation | Orientation of variant relative to reference |
| Haplotype | The haplotype of the variant |
| Score | log-likelihood score for variant |
| PassFilter | PASS if passes internal NAIBR filter
threshold, otherwise FAIL |
| SV | The type of variant (inversion, deletion, or duplication) |
The table below details the variants detected by NAIBR that appear on a single contig/chromosome and passed the programs internal filtering.
The table below shows any structural variants whose breakpoints span multiple contigs and may require further assessment. These variants are not shown in the plots below.
Below are three circular plots to visualize the distribution of putative structural variants across (up to) 30 of the largest contigs across the groups you specified in your data. If you are unfamiliar with this kind of visualization, it’s a circular version of a linear genome. Each “wedge” is a different contig, from position 0 to the end of the contig, and is labelled by the contig name. Each internal (grey) ring is a plot of observed structural variants for that contig for a different population.
Very small variants may be difficult to see or will not appear on the plot. Deletions are displayed as points as they tend to be small and clump together. You may hover your cursor over variants to view their positions, pan by clicking and dragging, and zoom using scroll (mouse or touchpad). In case you become unable to scroll up from the plot due to these interactive features, place your cursor over the navigation bar of this report and you will be able to scroll the report instead of zooming on the plot.